| Variant ID: vg0234179766 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 34179766 |
| Reference Allele: ACGTAATG | Alternative Allele: A |
| Primary Allele: ACGTAATG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTAAGTTTTTAACCGATGCAGACCATCAGTGGAATGCCACTTATTTTATTTTAAAGGTTGTATTACCTTACAAGGATTTACTTACTGTTTTCCTTCAAAC[ACGTAATG/A]
GCCCAAAAAACAGTGACGGCCAGCCAATACTGACTGATCATACCTGGCACATTGTTGAAAGGTTCAATCAATTTCTTGAAACGTTTCATGACTGTACTCT
AGAGTACAGTCATGAAACGTTTCAAGAAATTGATTGAACCTTTCAACAATGTGCCAGGTATGATCAGTCAGTATTGGCTGGCCGTCACTGTTTTTTGGGC[CATTACGT/T]
GTTTGAAGGAAAACAGTAAGTAAATCCTTGTAAGGTAATACAACCTTTAAAATAAAATAAGTGGCATTCCACTGATGGTCTGCATCGGTTAAAAACTTAC
| Populations | Population Size | Frequency of ACGTAATG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.80% | 0.30% | 7.66% | 37.24% | NA |
| All Indica | 2759 | 31.20% | 0.30% | 9.68% | 58.90% | NA |
| All Japonica | 1512 | 97.80% | 0.10% | 0.13% | 1.98% | NA |
| Aus | 269 | 58.00% | 0.00% | 25.28% | 16.73% | NA |
| Indica I | 595 | 22.40% | 0.00% | 5.55% | 72.10% | NA |
| Indica II | 465 | 22.20% | 0.20% | 4.95% | 72.69% | NA |
| Indica III | 913 | 38.10% | 0.50% | 16.87% | 44.47% | NA |
| Indica Intermediate | 786 | 35.10% | 0.10% | 7.25% | 57.51% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.13% | 2.09% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.40% | 0.41% | 4.56% | NA |
| VI/Aromatic | 96 | 33.30% | 8.30% | 14.58% | 43.75% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 12.22% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234179766 | ACGTAATG -> A | LOC_Os02g55840.1 | upstream_gene_variant ; 2318.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179766 | ACGTAATG -> A | LOC_Os02g55840.2 | upstream_gene_variant ; 2318.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179766 | ACGTAATG -> A | LOC_Os02g55840.5 | upstream_gene_variant ; 2318.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179766 | ACGTAATG -> A | LOC_Os02g55840.4 | upstream_gene_variant ; 2318.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179766 | ACGTAATG -> A | LOC_Os02g55840.3 | upstream_gene_variant ; 2318.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179766 | ACGTAATG -> A | LOC_Os02g55840.6 | upstream_gene_variant ; 2320.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179766 | ACGTAATG -> A | LOC_Os02g55830.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179766 | ACGTAATG -> DEL | N | N | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |